This chapter introduces you to the usage of so called 'Molecule
Profiles'. Such profiles describe the conformation and even the
granularity of a specific molecule, which you can define by
yourself. In this way, you are able to apply an alternative conformation
and/or granularity to a molecule and so to change the defaults given by
the molecule's pdb-file.
Molecule Profiles can be generated, edited and finally applied by the
Molecule Editor, which can be accessed by pressing 'Select Profile' in
an entry inside the Component View or by pressing 'Manage
Molecule Profiles' in the Local Database View:
The Molecule Editor looks the this:
Here you can switch between two modes: 'Edit Conformation' and 'Coarse
Grain'. "Coarse Graining" is a popular approach of simplifying
molecules to allow more efficient simulations and means a
reduction of the actual number of atoms by reducing groups of atoms
into a single particle.
Why edit conformations?
The default conformation, especially of lipids may be quite unpleasant
(shown in the picture above). You can either look for a pdb file with a
more suitable conformation, or you can edit the conformation here by
The advantage is that you can define different conformations in different profiles without needing multiple pdb files.
Why edit the granularity?
This has three reasons:
(1) You want to create a membrane that
serves as an initial state in further molecular simulation. It could
make sense to use this option as a coarse-grain approach, assuming that
the simulation is aware of the particles that have been made.
(2) You want to create more simple membranes for simulation and visualization tools,
such as the virtual cell, where a reduced number of atoms widely
effects the performance (note that fewer atoms, respectively with
longer distances between them will still be regarded as bonded if they
have been bonded before. Due to the CONECT's written into the
final pdb file those bonds remain and should be properly displayed by
most pdb viewers).
(3) You can also benefit from simplified molecules
if you are using the Atom Level Minimizer algorithm
where the speed of the calculation also depends significantly on the total number of involved atoms.
A profile for the viewed molecule can be chosen in the upper toolbar
of the Molecule Editor. If any changes have been made, you will also be
able to save the current profile or to save it as a new one. Simply use
the button 'Save Only' for this task. Enter a new name in order to
create a new profile or enter the name of any existing profile to
overwrite it. The 'Default Profile' cannot be changed. Stored
profiles will always be available for the specific type of molecule,
independently of the currently opened Membrane Model.
This option is only available if the Molecule Editor has been opened
from inside the Component View, meaning that you refer to a group of
molecules that have already been added to the membrane. By applying a
profile, all regarded instances inside the membrane will change their
conformation and/or granularity according to the selected profile.
Click 'Apply Profile' on the left side in the upper toolbar or 'Save and Apply' if any changes have been made.
You will see another dialog where you have to specify the members that you want to apply to: